# NM_033028.5(BBS4):c.217del (p.Gln73fs)

https://sugi.bio/variant/bbs4-p-gln73fs

## Summary

**BBS4 p.Gln73fs (c.217del)** is classified **Pathogenic** in BBS4 (ClinVar, Single submitter, 1 submitter). No gnomAD frequency available for this variant; Associated with Bardet-Biedl syndrome.

**At a glance:** Pathogenic · review: Single submitter · rsID rs2542940636 · 1 submitter · 1 linked condition · no gnomAD frequency available for this variant

## For patients & families {#patients}

This is a change in the BBS4 gene that is reported as disease-causing, but on limited review, submitted by 1 submitter, and is linked to Bardet-Biedl syndrome.

*Reference information, not medical advice, and not a prediction for any individual. A genetic counselor or clinician can interpret what it means for you and your family.*

|  |  |
| --- | --- |
| Typical inheritance (of this condition) | Autosomal recessive, Oligogenic |
| Age of onset (of this condition) | Antenatal, Childhood, Infancy, Neonatal |
| Prevalence | 1-9 / 100 000 (Specific population) |
| Clinical trials | 18 registered for this condition — see ClinicalTrials.gov |
| Diagnostic panels | BBS4 is a diagnostic-grade gene on 17 Genomics England panels |

**Commonly reported features of Bardet-Biedl syndrome** (across patients with this condition; presentation varies — frequencies from Orphanet):

- Retinal dystrophy — Obligate (100%)
- Cone/cone-rod dystrophy — Very frequent (99-80%)
- Obesity — Very frequent (99-80%)
- Childhood-onset truncal obesity — Very frequent (99-80%)
- Neurodevelopmental delay — Very frequent (99-80%)
- Abnormality of the genitourinary system — Frequent (79-30%)
- Hypogonadism — Frequent (79-30%)
- Abnormal oral cavity morphology — Frequent (79-30%)

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0006866/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [BBS4](https://sugi.bio/atlas/gene/BBS4/) |
| Protein change (HGVS p.) | p.Gln73fs |
| Coding change (HGVS c.) | c.217del |
| MANE Select transcript | [NM_033028](https://www.ncbi.nlm.nih.gov/nuccore/NM_033028) |
| dbSNP | [rs2542940636](https://www.ncbi.nlm.nih.gov/snp/rs2542940636/) |
| Variant type | Deletion |
| Location | chr15:72712303-72712303 (GRCh38) |
| ClinVar | [VCV2498298](https://www.ncbi.nlm.nih.gov/clinvar/variation/2498298/) |

**All HGVS expressions:** `NC_000015.10:g.72712304del`, `NC_000015.9:g.73004645del`, `NG_009416.2:g.31120del`, `NG_009416.3:g.31099del`, `NM_001252678.2:c.-305del`, `NM_001320665.2:c.217del`, `NM_033028.5:c.217del`, `NR_045565.2:n.296del`, `NR_045566.2:n.551del`

## Computational & population evidence {#evidence}

**Concordance:** 1 independent predictor **concordant** with the ClinVar classification.

- **Missense predictors (AlphaMissense/REVEL/SaProt) do not apply** to this variant type — they score amino-acid substitutions only. For non-missense variants the computational signal comes from conservation (below), not from a missing predictor score.
- Conservation: phyloP 7.822, GERP 1.4, phastCons 1 — highly conserved position (PP3-type support)
- Molecular consequence: **frameshift** — a predicted loss-of-function variant. Gene population constraint: LOEUF 0.953, pLI 6.813e-12. *Descriptive; not an applied PVS1 code.*
- Nonsense-mediated decay: the premature termination codon is **in exon 4 of 16**, so the transcript is predicted to undergo NMD.
- SpliceAI: **not assessed** — the release is built from a substitutions-only source, so it holds no deletion variants. That is a property of the dataset, not of the variant, and is not evidence against a splicing effect.
- Population frequency: **no gnomAD frequency available for this variant** — rarity (ACMG PM2) and BA1/BS1 cannot be assessed for this variant.

*Computational predictors are not independent (ClinGen Variant Classification guidance): AlphaMissense (Cheng et al. 2023) carries the ACMG weight for missense and conservation (phyloP/GERP/phastCons) for non-missense; REVEL (Pejaver-2022 calibrated strength bands) and SaProt (Su et al. 2023, structure-aware, ClinVar-independent protein language model, raw LLR) are shown as orthogonal agreement signals, not additive. For frequency, the gnomAD v4.1 grpmax filtering allele frequency (FAF95) is ClinGen's designated BA1/BS1 input (gnomAD v4 guidance v3.0, June 2025); BA1/BS1 thresholds are disease-specific, not a blanket 5%. Predictions, not a clinical determination.*

## Gene constraint & dosage {#gene-context}

**BBS4** population constraint: LOEUF 0.953, pLI 6.813e-12, missense-Z -0.37523. *Lower LOEUF and higher pLI indicate a gene that tolerates loss-of-function poorly; ClinGen dosage is the curated haploinsufficiency call.*

Curated gene–disease validity (ClinGen):

- **BBS4-related ciliopathy** — Definitive (AR)

## Protein context {#protein}


AlphaFold model confidence (whole protein): pLDDT 78.36, 59% of residues very-high.

**1 experimental structure(s)** (PDB): [6XT9](https://www.rcsb.org/structure/6XT9).

## What this gene does {#gene-function}

*Describes the biological roles of BBS4 (the gene this variant disrupts) — not effects measured for this specific variant. A damaging variant is expected to affect these functions and pathways; the degree depends on the variant.*

**How this variant is thought to act:** BBS4's established molecular role includes protein-macromolecule adaptor activity.


### Pathways affected {#pathways}

BBS4 participates in **1 Reactome pathway** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [BBSome-mediated cargo-targeting to cilium](https://reactome.org/content/detail/R-HSA-5620922) | curated |

### Molecular function & processes (GO — experimentally supported) {#go}

**Molecular function:** protein-macromolecule adaptor activity, dynactin binding, alpha-tubulin binding, beta-tubulin binding, RNA polymerase II-specific DNA-binding transcription factor binding.

**Biological process:** mitotic cytokinesis, centrosome cycle, regulation of cytokinesis, microtubule anchoring at centrosome, maintenance of protein location in nucleus, protein localization to cilium.

## Clinical significance {#significance}

**Pathogenic** — review status Single submitter *(criteria provided, single submitter)*.

**Submitter consensus:** unanimous (1/1 Pathogenic).

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| SN ONGC Dept of Genetics and Molecular biology Vision Research Foundation | Pathogenic | criteria provided, single submitter | research |  |

## Associated conditions {#conditions}

[Bardet-Biedl syndrome](https://sugi.bio/atlas/disease/bardet-biedl-syndrome/).

**Reported phenotype names (ClinVar):** Bardet-Biedl syndrome.

## Similar variants {#similar}

Related BBS4 variant pages (same residue, condition, or type): [BBS4 c.1064_1106+97del](/variant/bbs4-c-1064-1106-plus-97del), [BBS4 p.Glu432fs](/variant/bbs4-p-glu432fs), [BBS4 p.Leu114fs](/variant/bbs4-p-leu114fs), [BBS4 p.Leu310fs](/variant/bbs4-p-leu310fs), [BBS4 p.Leu381fs](/variant/bbs4-p-leu381fs), [BBS4 p.Lys358fs](/variant/bbs4-p-lys358fs), [BBS4 p.Pro30fs](/variant/bbs4-p-pro30fs), [BBS4 p.Ser409fs](/variant/bbs4-p-ser409fs).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-11); gnomAD v4.1 (Broad Institute, built 2026-10-06); AlphaMissense (Cheng et al. 2023, © Google DeepMind — CC BY 4.0, built 2026-01-27); REVEL (Ioannidis et al. 2016 — ODbL, built 2026-07-13); SaProt (Su et al. 2023 — MIT, built 2026-07-14); SpliceAI (Illumina — free for non-commercial use, built 2026-10-13); CADD (Rentzsch et al. 2019, University of Washington — free for non-commercial use, built 2026-10-10); Conservation (phyloP/phastCons/GERP) (UCSC hg38 470-way mammal (Hiller Lab) + Ensembl Compara, built 2026-07-12); gnomAD Non-coding Constraint (Gnocchi) (Chen et al. 2024, Broad Institute — CC0, built 2026-10-11); gnomAD Regional Missense Constraint (Broad Institute — CC0, built 2026-10-13); Pangolin (Zeng & Li 2022 — CC BY 4.0, built 2026-10-11); Repeat regions (UCSC — RepeatMasker, TRF, segmental duplications, built 2026-10-11); ClinGen (ClinGen, built 2026-09-22); UniProt (CC BY 4.0); Reactome / GO (CC BY 4.0, built 2026-09-23); MaveDB (per-record license, built 2026-10-11); CIViC (CC0, built 2026-09-22); Orphanet (Orphanet, built 2026-06-12)

*Primary record: NCBI ClinVar (variation 2498298). Classifications reflect these databases as of the page's build date and may change. Free reference use — not medical advice; consult the primary submitters and a clinician.*